President Bush's drive for absolute power has momentarily stalled. In a single coup, he planned to take over all the institutions of government. By crushing the traditions of the Senate he would pack the courts, especially the supreme court, with lockstep ideologues. Sheer force would prevail. But just as his blitzkrieg reached the outskirts of his objective, he was struck by a mutiny. Within the span of 24 hours he lost control not only of the Senate but temporarily of the House of Representatives, which was supposed to be regimented by unquestioned loyalty. Now he prepares to launch a counterattack - against the dissident elements of his own party.

Bush's wonder weapon for total victory was a device called the "nuclear option". Once it was triggered, it would obliterate a 200-year-old tradition of the Senate. The threat of a Democratic filibuster in the Senate of his appointments to the federal bench would set the doomsday sequence in motion. The Senate Republican majority leader, Bill Frist of Tennessee, would call for a change in the rule, and a simple majority would vote to abolish the filibuster. Bush's nominees would sail through.

Unlike the House, the Senate was constructed by the constitutional framers as an unrepresentative body, with each state, regardless of population, allotted two senators. Currently, the Republicans have 55 senators who represent only 45% of the country. The Senate creates its own rules, and the filibuster can only be stopped by a super-majority of 60 votes. Historically, it was used by southern senators to block civil rights legislation. In the first two years of the Clinton presidency, the Republicans deployed 48 filibusters, more than in the entire previous history of the Senate, to make the new Democratic chief executive appear feckless. The strategy was instrumental in the Republican capture of the Congress in 1994. By depriving the Democrats of the filibuster, Bush intended to transform the Senate into his rubber stamp.

For many senators the fate of the filibuster was only superficially about an arcane rule change. And shameless hypocrisy was the least of the problem. (Frist, like most Republicans in favour of the nuclear option, had enthusiastically filibustered against Clinton's court nominees, 65 of which were blocked from 1995-2000.) If Bush succeeded he would have effectively removed the Senate's "advice and consent" on executive appointments, drastically reducing its power.

Over the weekend, two elders, Senator Robert Byrd, Democrat of West Virginia, and Senator John Warner, Republican of Virginia, pored over the federalist papers, written by the constitutional framers, to refresh their thinking about the inviolability of the Senate. On Monday, seven Republicans and seven Democrats signed a pact that preserved the filibuster under "extraordinary" circumstances and allowed several of Bush's appointments to be voted on.

The mutiny is broader than is apparent. More than the seven Republican signatories supported the accord, but they let the others take a public stance without revealing themselves. Bush's radicalism offended their conservatism. Eisenhower would be their preferred model for a Republican president. These Republican senators are the equivalent of the Republicans on the supreme court, Sandra Day O'Connor and Anthony Kennedy, who are conservative but operate without ideology, and hold the balance against the aggressive rightwing justices.

The day after Bush was frustrated by Republicans in the Senate, 50 Republicans in the House deserted him on the issue of stem cell research. His policy limiting scientific work is a sop to the religious right that views the stem cell question as an extension of abortion. Debate in the House was marshalled by Republican majority leader Tom DeLay, who argued that Bush's policy must be supported because "Jesus of Nazareth" began life as an embryo. Bush promised to veto the stem cell bill passed with massive Republican defections, the irony of his opposition to the filibuster unmentioned.

The compromise pact in the Senate on the filibuster hardly postpones the coming storms. The White House intends to push judicial nominees that the Democrats are almost certain to filibuster. With the elimination of the nuclear option, the filibuster may also be used against Bush's supreme court appointments. Evangelical religious right leaders denounce Republican senators as sell-outs. One of the most influential, James Dobson, has cursed one of the silent compromise supporters, Senator Trent Lott, the former Republican majority leader from Mississippi, as a Judas, and Lott has called Dobson "quite unChristian".

Meanwhile, the conflict has focused attention on the Republican presidential succession of 2008, pitting Bill Frist - positioning himself as the darling of the right - against cantankerous John McCain, one of the Republican magnificent seven. Within the party, metal is scraping on metal. But the more the resistance, the more Bush presses forward. His unilateralism abroad has been brought home, with a vengeance, to his partisan wars.

In federalist paper number 69 (perhaps re-read by Byrd and Warner), Alexander Hamilton concludes his examination of the differences between the "qualified" powers of the US presidency and the "absolute" powers of the king of Great Britain: "The one has no particle of spiritual jurisdiction; the other is the supreme head and governor of the national church! What answer shall we give to those who would persuade us that things so unlike resemble each other? The same that ought to be given to those who tell us that a government, the whole power of which would be in the hands of the elective and periodical servants of the people, is an aristocracy, a monarchy, and a despotism."

· Sidney Blumenthal is former senior adviser to President Clinton and author of The Clinton Wars